Hi Antonella, the argument to --annot has to be an annotation file (something.annot). mri_glmfit-sim should generate an annot file. If you are running mri_surfcluster to get ocn.mgh, it will also generate an annot file. doug
On 8/27/12 8:31 PM, Antonella Kis wrote:
Hi,
I am trying to run the mri_label2vol but I am getting the following error. I am not sure which annot file I should use for my QDEC clusters. I tried to use my annot file from mri_glmfit-sim but it didn't work. I was running:
mri_label2vol --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --fillthresh 0 --subject fsaverage --hemi lh --annot /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh --o /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/sig2MNI.nii
and my error:
Number of labels: 0 Annot File: /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh Template Volume: MNI152_T1_1mm_brain.nii.gz Outut Volume: /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/sig2MNI.nii Registration File: /usr/local/freesurfer//average/mni152.register.dat Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: fsaverage Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.34.2.1 2011/03/22 18:09:04 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 91.000; -0.000 -0.000 -1.000 109.000; -0.000 1.000 -0.000 91.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Loading registration from /usr/local/freesurfer//average/mni152.register.dat RegMat: -------- 0.998 -0.007 0.018 0.957; -0.013 -0.009 0.997 -17.816; -0.015 -1.001 0.002 -18.550; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -0.998 0.007 -0.018 90.043; 0.015 1.001 -0.002 127.550; -0.013 -0.009 0.997 73.184; 0.000 0.000 0.000 1.000; INFO: loading surface /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/fsaverage/surf/lh.white nvertices = 163842 Reading thickness /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/qdec/lh_L_FrontalEpilepsy/lh-Avg-Intercept-thickness/fsaverage/surf/lh.thickness Loading annotations from /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh MRISreadAnnotationIntoArray: vertex index out of range: 163842 i=00000001, in_array_size=163842 annot file: /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh reading colortable from annotation file... colortable with 1 entries read (originally ) annotidmax = 0 ERROR: load annot file /media/2Tra/Antonella_Backup/Antonella_2011/DTI_FLE_NPI/FLE_FS_QDEC/lh.L_frontal.glmdir/lh-Avg-thickness-Cor/ocn.mgh
Thanks, AK
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